Balkan Medical Journal currently indexed in;

Science Citation Index Expanded (Web of Science)
Journal Citation Reports
PubMed/MEDLINE
PubMed Central
Scopus
EMBASE
DOAJ
Chemical Abstracts
CINAHL
EBSCO
CABI Abstracts and Bibliographic Databases
J-Gate
GALE
ProQuest
Türk Medline
IdealOnline
Global Health
UDL-EDGE
Hinari
GOALI
ARDI
OARE
AGORA
TÜBİTAK ULAKBİM TR Index
CNKI