Salmonellosis is one of the most frequent food-borne infections. It is caused by infected food mainly of animal origin, although human to human transmission and numerous environmental contaminations may also be inflicted. Salmonella enterica serovar Enteritidis (S. Enteritidis) is a common pathogen worldwide. In this study 49 S. Enteritidis isolates from veterinary and food sources in Bulgaria obtained during the years 2004 to 2012 were analysed. The multiple-locus variable-number of tandem repeats analysis (MLVA) genotyping and the antimicrobial resistance (AMR) to compare the isolates were used. Results showed that isolates were divided into twenty-four MLVA and nine AMR profiles. The calculated Simpson's diversity index was 0.956 for MLVA and 0.693 to be changed for AMR, respectively. The most frequent MLVA profiles presented according to the order of the loci sequenced SENTR7 - SENTR5 - SENTR6 - SENTR4 - SE-3 were: 3-11-5-3-3 (n = 6); 2-8-9-5-3 (n = 5); 2-11-13-5-3 (n = 5); 2-11-12-6-3 (n = 4); 2-11-10-5-3 (n = 3); 3- 9-5-4-3 (n = 3). The AMR revealed that 53.1% of the isolates were resistant to one and 4.1% to ≥ 4 antimicrobials. The MLVA profiles obtained in this study were compared to the published data and they have not been isolated on a frequent basis. A partial match was found for isolates in Belgium, Thailand, China, and USA only.