Background and Objectives: Effectiveness of prophylactic antibiotics is based on the susceptibility of the common potential pathogens to those antibiotics. Irrational use of drugs has an adverse impact on treatment outcome and financial burden to patients. Aims: Objective of this study was to evaluate the effect of antibiotic prophylaxis on surgical site infections and wound colonisation. Materials and Methods: A cross-sectional study was conducted among the patients of general surgery wards of a tertiary care hospital of central Kerala. Swabs collected from surgical wound sites after 48 h of surgery were analysed for bacteriological profile and antibiotic prophylaxis given. Statistical analysis was done by Epi Info. Results: Three hundred and ten cases were studied including 75.5% elective and 24.5% emergency cases. Cefotaxime (55.2%) and third generation cephalosporin combination with β-lactamase inhibitors (35.5%) were commonly used for antibiotic prophylaxis. Infection rates were 2.1% in clean surgeries, 8.1% in clean-contaminated and 22.8% in contaminated types of surgeries with an overall infection rate of 8.1%. Escherichia coli (45%) and Staphylococcus aureus (34.5%) were the predominant wound pathogens. Colonisation in 28.1% wounds with S. aureus as the major coloniser (72.8%) was noticed. Susceptibility of E. coli to Cefotaxime was 15.4% in infections and 20% in colonisation. Infection rates were higher in the group with multiple antibiotic usages for 5 days (40%) or above (52%). Colonisation increased on prolonged administration of multiple antibiotics (40%) and without using antibiotics (39%). Clean wounds without antibiotic prophylaxis were not infected. Conclusions: This study revealed that antibiotic prophylaxis is not required for clean wounds. Short duration of antibiotics usage based on the local susceptibility pattern is to be adopted. Antibiotic usage has to be restricted, and prophylactic regime with third-generation cephalosporin has to be curtailed.