diff --git a/jvm-packages/xgboost4j/src/native/xgboost4j.cpp b/jvm-packages/xgboost4j/src/native/xgboost4j.cpp
index 8b08a869f..de0383143 100644
--- a/jvm-packages/xgboost4j/src/native/xgboost4j.cpp
+++ b/jvm-packages/xgboost4j/src/native/xgboost4j.cpp
@@ -556,11 +556,12 @@ JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_java_XGBoostJNI_XGBoosterPredict
   bst_ulong len;
   float *result;
   int ret = XGBoosterPredict(handle, dmat, joption_mask, (unsigned int) jntree_limit, &len, (const float **) &result);
-
-  jsize jlen = (jsize) len;
-  jfloatArray jarray = jenv->NewFloatArray(jlen);
-  jenv->SetFloatArrayRegion(jarray, 0, jlen, (jfloat *) result);
-  jenv->SetObjectArrayElement(jout, 0, jarray);
+  if (len) {
+    jsize jlen = (jsize) len;
+    jfloatArray jarray = jenv->NewFloatArray(jlen);
+    jenv->SetFloatArrayRegion(jarray, 0, jlen, (jfloat *) result);
+    jenv->SetObjectArrayElement(jout, 0, jarray);
+  }
   return ret;
 }
 
diff --git a/src/c_api/c_api.cc b/src/c_api/c_api.cc
index 569fff016..d5d1747db 100644
--- a/src/c_api/c_api.cc
+++ b/src/c_api/c_api.cc
@@ -650,6 +650,7 @@ XGB_DLL int XGDMatrixSliceDMatrix(DMatrixHandle handle,
   std::unique_ptr<data::SimpleCSRSource> source(new data::SimpleCSRSource());
 
   API_BEGIN();
+  CHECK_HANDLE();
   data::SimpleCSRSource src;
   src.CopyFrom(static_cast<std::shared_ptr<DMatrix>*>(handle)->get());
   data::SimpleCSRSource& ret = *source;
@@ -694,6 +695,7 @@ XGB_DLL int XGDMatrixSliceDMatrix(DMatrixHandle handle,
 
 XGB_DLL int XGDMatrixFree(DMatrixHandle handle) {
   API_BEGIN();
+  CHECK_HANDLE();
   delete static_cast<std::shared_ptr<DMatrix>*>(handle);
   API_END();
 }
@@ -702,6 +704,7 @@ XGB_DLL int XGDMatrixSaveBinary(DMatrixHandle handle,
                                 const char* fname,
                                 int silent) {
   API_BEGIN();
+  CHECK_HANDLE();
   static_cast<std::shared_ptr<DMatrix>*>(handle)->get()->SaveToLocalFile(fname);
   API_END();
 }
@@ -711,6 +714,7 @@ XGB_DLL int XGDMatrixSetFloatInfo(DMatrixHandle handle,
                           const bst_float* info,
                           xgboost::bst_ulong len) {
   API_BEGIN();
+  CHECK_HANDLE();
   static_cast<std::shared_ptr<DMatrix>*>(handle)
       ->get()->Info().SetInfo(field, info, kFloat32, len);
   API_END();
@@ -721,6 +725,7 @@ XGB_DLL int XGDMatrixSetUIntInfo(DMatrixHandle handle,
                          const unsigned* info,
                          xgboost::bst_ulong len) {
   API_BEGIN();
+  CHECK_HANDLE();
   static_cast<std::shared_ptr<DMatrix>*>(handle)
       ->get()->Info().SetInfo(field, info, kUInt32, len);
   API_END();
@@ -730,6 +735,7 @@ XGB_DLL int XGDMatrixSetGroup(DMatrixHandle handle,
                               const unsigned* group,
                               xgboost::bst_ulong len) {
   API_BEGIN();
+  CHECK_HANDLE();
   auto *pmat = static_cast<std::shared_ptr<DMatrix>*>(handle);
   MetaInfo& info = pmat->get()->Info();
   info.group_ptr_.resize(len + 1);
@@ -745,6 +751,7 @@ XGB_DLL int XGDMatrixGetFloatInfo(const DMatrixHandle handle,
                                   xgboost::bst_ulong* out_len,
                                   const bst_float** out_dptr) {
   API_BEGIN();
+  CHECK_HANDLE();
   const MetaInfo& info = static_cast<std::shared_ptr<DMatrix>*>(handle)->get()->Info();
   const std::vector<bst_float>* vec = nullptr;
   if (!std::strcmp(field, "label")) {
@@ -766,6 +773,7 @@ XGB_DLL int XGDMatrixGetUIntInfo(const DMatrixHandle handle,
                                  xgboost::bst_ulong *out_len,
                                  const unsigned **out_dptr) {
   API_BEGIN();
+  CHECK_HANDLE();
   const MetaInfo& info = static_cast<std::shared_ptr<DMatrix>*>(handle)->get()->Info();
   const std::vector<unsigned>* vec = nullptr;
   if (!std::strcmp(field, "root_index")) {
@@ -781,6 +789,7 @@ XGB_DLL int XGDMatrixGetUIntInfo(const DMatrixHandle handle,
 XGB_DLL int XGDMatrixNumRow(const DMatrixHandle handle,
                             xgboost::bst_ulong *out) {
   API_BEGIN();
+  CHECK_HANDLE();
   *out = static_cast<xgboost::bst_ulong>(
       static_cast<std::shared_ptr<DMatrix>*>(handle)->get()->Info().num_row_);
   API_END();
@@ -789,6 +798,7 @@ XGB_DLL int XGDMatrixNumRow(const DMatrixHandle handle,
 XGB_DLL int XGDMatrixNumCol(const DMatrixHandle handle,
                             xgboost::bst_ulong *out) {
   API_BEGIN();
+  CHECK_HANDLE();
   *out = static_cast<size_t>(
       static_cast<std::shared_ptr<DMatrix>*>(handle)->get()->Info().num_col_);
   API_END();
@@ -809,6 +819,7 @@ XGB_DLL int XGBoosterCreate(const DMatrixHandle dmats[],
 
 XGB_DLL int XGBoosterFree(BoosterHandle handle) {
   API_BEGIN();
+  CHECK_HANDLE();
   delete static_cast<Booster*>(handle);
   API_END();
 }
@@ -817,6 +828,7 @@ XGB_DLL int XGBoosterSetParam(BoosterHandle handle,
                               const char *name,
                               const char *value) {
   API_BEGIN();
+  CHECK_HANDLE();
   static_cast<Booster*>(handle)->SetParam(name, value);
   API_END();
 }
@@ -825,6 +837,7 @@ XGB_DLL int XGBoosterUpdateOneIter(BoosterHandle handle,
                                    int iter,
                                    DMatrixHandle dtrain) {
   API_BEGIN();
+  CHECK_HANDLE();
   auto* bst = static_cast<Booster*>(handle);
   auto *dtr =
       static_cast<std::shared_ptr<DMatrix>*>(dtrain);
@@ -841,6 +854,7 @@ XGB_DLL int XGBoosterBoostOneIter(BoosterHandle handle,
                                   xgboost::bst_ulong len) {
   HostDeviceVector<GradientPair>& tmp_gpair = XGBAPIThreadLocalStore::Get()->tmp_gpair;
   API_BEGIN();
+  CHECK_HANDLE();
   auto* bst = static_cast<Booster*>(handle);
   auto* dtr =
       static_cast<std::shared_ptr<DMatrix>*>(dtrain);
@@ -863,6 +877,7 @@ XGB_DLL int XGBoosterEvalOneIter(BoosterHandle handle,
                                  const char** out_str) {
   std::string& eval_str = XGBAPIThreadLocalStore::Get()->ret_str;
   API_BEGIN();
+  CHECK_HANDLE();
   auto* bst = static_cast<Booster*>(handle);
   std::vector<DMatrix*> data_sets;
   std::vector<std::string> data_names;
@@ -887,6 +902,7 @@ XGB_DLL int XGBoosterPredict(BoosterHandle handle,
   HostDeviceVector<bst_float>& preds =
     XGBAPIThreadLocalStore::Get()->ret_vec_float;
   API_BEGIN();
+  CHECK_HANDLE();
   auto *bst = static_cast<Booster*>(handle);
   bst->LazyInit();
   bst->learner()->Predict(
@@ -904,6 +920,7 @@ XGB_DLL int XGBoosterPredict(BoosterHandle handle,
 
 XGB_DLL int XGBoosterLoadModel(BoosterHandle handle, const char* fname) {
   API_BEGIN();
+  CHECK_HANDLE();
   std::unique_ptr<dmlc::Stream> fi(dmlc::Stream::Create(fname, "r"));
   static_cast<Booster*>(handle)->LoadModel(fi.get());
   API_END();
@@ -911,6 +928,7 @@ XGB_DLL int XGBoosterLoadModel(BoosterHandle handle, const char* fname) {
 
 XGB_DLL int XGBoosterSaveModel(BoosterHandle handle, const char* fname) {
   API_BEGIN();
+  CHECK_HANDLE();
   std::unique_ptr<dmlc::Stream> fo(dmlc::Stream::Create(fname, "w"));
   auto *bst = static_cast<Booster*>(handle);
   bst->LazyInit();
@@ -922,6 +940,7 @@ XGB_DLL int XGBoosterLoadModelFromBuffer(BoosterHandle handle,
                                  const void* buf,
                                  xgboost::bst_ulong len) {
   API_BEGIN();
+  CHECK_HANDLE();
   common::MemoryFixSizeBuffer fs((void*)buf, len);  // NOLINT(*)
   static_cast<Booster*>(handle)->LoadModel(&fs);
   API_END();
@@ -934,6 +953,7 @@ XGB_DLL int XGBoosterGetModelRaw(BoosterHandle handle,
   raw_str.resize(0);
 
   API_BEGIN();
+  CHECK_HANDLE();
   common::MemoryBufferStream fo(&raw_str);
   auto *bst = static_cast<Booster*>(handle);
   bst->LazyInit();
@@ -976,6 +996,7 @@ XGB_DLL int XGBoosterDumpModelEx(BoosterHandle handle,
                        xgboost::bst_ulong* len,
                        const char*** out_models) {
   API_BEGIN();
+  CHECK_HANDLE();
   FeatureMap featmap;
   if (strlen(fmap) != 0) {
     std::unique_ptr<dmlc::Stream> fs(
@@ -1006,6 +1027,7 @@ XGB_DLL int XGBoosterDumpModelExWithFeatures(BoosterHandle handle,
                                    xgboost::bst_ulong* len,
                                    const char*** out_models) {
   API_BEGIN();
+  CHECK_HANDLE();
   FeatureMap featmap;
   for (int i = 0; i < fnum; ++i) {
     featmap.PushBack(i, fname[i], ftype[i]);
@@ -1021,6 +1043,7 @@ XGB_DLL int XGBoosterGetAttr(BoosterHandle handle,
   auto* bst = static_cast<Booster*>(handle);
   std::string& ret_str = XGBAPIThreadLocalStore::Get()->ret_str;
   API_BEGIN();
+  CHECK_HANDLE();
   if (bst->learner()->GetAttr(key, &ret_str)) {
     *out = ret_str.c_str();
     *success = 1;
@@ -1036,6 +1059,7 @@ XGB_DLL int XGBoosterSetAttr(BoosterHandle handle,
                      const char* value) {
   auto* bst = static_cast<Booster*>(handle);
   API_BEGIN();
+  CHECK_HANDLE();
   if (value == nullptr) {
     bst->learner()->DelAttr(key);
   } else {
@@ -1051,6 +1075,7 @@ XGB_DLL int XGBoosterGetAttrNames(BoosterHandle handle,
   std::vector<const char*>& charp_vecs = XGBAPIThreadLocalStore::Get()->ret_vec_charp;
   auto *bst = static_cast<Booster*>(handle);
   API_BEGIN();
+  CHECK_HANDLE();
   str_vecs = bst->learner()->GetAttrNames();
   charp_vecs.resize(str_vecs.size());
   for (size_t i = 0; i < str_vecs.size(); ++i) {
@@ -1064,6 +1089,7 @@ XGB_DLL int XGBoosterGetAttrNames(BoosterHandle handle,
 XGB_DLL int XGBoosterLoadRabitCheckpoint(BoosterHandle handle,
                                  int* version) {
   API_BEGIN();
+  CHECK_HANDLE();
   auto* bst = static_cast<Booster*>(handle);
   *version = rabit::LoadCheckPoint(bst->learner());
   if (*version != 0) {
@@ -1074,6 +1100,7 @@ XGB_DLL int XGBoosterLoadRabitCheckpoint(BoosterHandle handle,
 
 XGB_DLL int XGBoosterSaveRabitCheckpoint(BoosterHandle handle) {
   API_BEGIN();
+  CHECK_HANDLE();
   auto* bst = static_cast<Booster*>(handle);
   if (bst->learner()->AllowLazyCheckPoint()) {
     rabit::LazyCheckPoint(bst->learner());
diff --git a/src/c_api/c_api_error.h b/src/c_api/c_api_error.h
index 3c0899228..648a4b961 100644
--- a/src/c_api/c_api_error.h
+++ b/src/c_api/c_api_error.h
@@ -15,6 +15,8 @@
 /*! \brief every function starts with API_BEGIN();
      and finishes with API_END() or API_END_HANDLE_ERROR */
 #define API_END() } catch(dmlc::Error &_except_) { return XGBAPIHandleException(_except_); } return 0;  // NOLINT(*)
+#define CHECK_HANDLE() if (handle == nullptr) \
+  LOG(FATAL) << "DMatrix/Booster has not been intialized or has already been disposed.";
 /*!
  * \brief every function starts with API_BEGIN();
  *   and finishes with API_END() or API_END_HANDLE_ERROR