diff --git a/include/xgboost/c_api.h b/include/xgboost/c_api.h
index 787397ad9454..166ba833aec7 100644
--- a/include/xgboost/c_api.h
+++ b/include/xgboost/c_api.h
@@ -149,23 +149,6 @@ XGB_DLL int XGDMatrixCreateFromCSREx(const size_t* indptr,
                                      size_t nelem,
                                      size_t num_col,
                                      DMatrixHandle* out);
-/*!
- * \deprecated
- * \brief create a matrix content from CSR format
- * \param indptr pointer to row headers
- * \param indices findex
- * \param data fvalue
- * \param nindptr number of rows in the matrix + 1
- * \param nelem number of nonzero elements in the matrix
- * \param out created dmatrix
- * \return 0 when success, -1 when failure happens
- */
-XGB_DLL int XGDMatrixCreateFromCSR(const bst_ulong *indptr,
-                                   const unsigned *indices,
-                                   const float *data,
-                                   bst_ulong nindptr,
-                                   bst_ulong nelem,
-                                   DMatrixHandle *out);
 /*!
  * \brief create a matrix content from CSC format
  * \param col_ptr pointer to col headers
@@ -184,23 +167,7 @@ XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
                                      size_t nelem,
                                      size_t num_row,
                                      DMatrixHandle* out);
-/*!
- * \deprecated
- * \brief create a matrix content from CSC format
- * \param col_ptr pointer to col headers
- * \param indices findex
- * \param data fvalue
- * \param nindptr number of rows in the matrix + 1
- * \param nelem number of nonzero elements in the matrix
- * \param out created dmatrix
- * \return 0 when success, -1 when failure happens
- */
-XGB_DLL int XGDMatrixCreateFromCSC(const bst_ulong *col_ptr,
-                                   const unsigned *indices,
-                                   const float *data,
-                                   bst_ulong nindptr,
-                                   bst_ulong nelem,
-                                   DMatrixHandle *out);
+
 /*!
  * \brief create matrix content from dense matrix
  * \param data pointer to the data space
diff --git a/src/c_api/c_api.cc b/src/c_api/c_api.cc
index cb7240448e5b..9092918031c7 100644
--- a/src/c_api/c_api.cc
+++ b/src/c_api/c_api.cc
@@ -304,20 +304,6 @@ XGB_DLL int XGDMatrixCreateFromCSREx(const size_t* indptr,
   API_END();
 }
 
-XGB_DLL int XGDMatrixCreateFromCSR(const xgboost::bst_ulong* indptr,
-                                   const unsigned *indices,
-                                   const bst_float* data,
-                                   xgboost::bst_ulong nindptr,
-                                   xgboost::bst_ulong nelem,
-                                   DMatrixHandle* out) {
-  std::vector<size_t> indptr_(nindptr);
-  for (xgboost::bst_ulong i = 0; i < nindptr; ++i) {
-    indptr_[i] = static_cast<size_t>(indptr[i]);
-  }
-  return XGDMatrixCreateFromCSREx(&indptr_[0], indices, data,
-    static_cast<size_t>(nindptr), static_cast<size_t>(nelem), 0, out);
-}
-
 XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
                                      const unsigned* indices,
                                      const bst_float* data,
@@ -374,20 +360,6 @@ XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
   API_END();
 }
 
-XGB_DLL int XGDMatrixCreateFromCSC(const xgboost::bst_ulong* col_ptr,
-                                   const unsigned* indices,
-                                   const bst_float* data,
-                                   xgboost::bst_ulong nindptr,
-                                   xgboost::bst_ulong nelem,
-                                   DMatrixHandle* out) {
-  std::vector<size_t> col_ptr_(nindptr);
-  for (xgboost::bst_ulong i = 0; i < nindptr; ++i) {
-    col_ptr_[i] = static_cast<size_t>(col_ptr[i]);
-  }
-  return XGDMatrixCreateFromCSCEx(&col_ptr_[0], indices, data,
-    static_cast<size_t>(nindptr), static_cast<size_t>(nelem), 0, out);
-}
-
 XGB_DLL int XGDMatrixCreateFromMat(const bst_float* data,
                                    xgboost::bst_ulong nrow,
                                    xgboost::bst_ulong ncol,