Background: Salmonella infections are of serious public health concern since these bacteria frequently cause foodborne illness, human gastroenteritis and bacteremia worldwide. Though invasive salmonella are uncommon in developed nations it is still common in developing countries. Salmonella is frequently isolated in Cape coast Hospital and are often found to be drug resistant. This study therefore determined the antimicrobial susceptibility and PFGE patterns of Salmonella and other gram negative organisms isolated. Methods: Cross-sectional study involving 971 samples (463 blood and 508 stool) was carried out over 13 month period. Isolates were identified and antimicrobial susceptibility test performed. The Salmonellae were serotyped and ESBL and fingerprinted by PFGE. Data obtained was analyzed with SPSS Version 21.0 taking confidence level of 95% and p values<0.05. Results: A total of 17 Salmonellae being 3.3% and 3 Shigella flexneri recording 0.6% were recovered from the stool samples. The Salmonella serovars encountered were Salmonella Typhi (13/17) and Salmonella Typhimurium (4/17). There was 82% multidrug resistance among the Salmonellae with none producing ESBL. The PFGE analysis of the similar Salmonella serovars indicated they were different clones. Blood samples yielded different bacteria types (69/463, 14.9%) other than Salmonella. Conclusion: Salmonella was not obtained from blood but was obtained from stool with 3.3% prevalence. There was a high prevalence of bacteremia caused by other pathogens recording 14.9%. There was high multidrug resistance rate of 98.6% among the blood isolates and 82% among the Salmonella isolates.