Sheep (BW = 39.9 kg, n = 16) and goats (BW = 32.8 kg, n = 16) were used in a completely randomized design to determine the effect of short-term pre-slaughter diet and feed deprivation (FD) time on pH and microbial loads in the gastrointestinal tract (GIT) contents. In a 2 × 2 × 2 factorial treatment arrangement, the main effects of species, diet, and FD time prior to slaughter and their interactions were studied. Animals were fed either a hay or concentrate diet for 4 d and then feed deprived for either 12 or 24-h prior to slaughter. The pH of rumen and colon contents as well as weight of GIT was measured. The contents of rumen and rectum were also sampled for microbial analysis. The GIT of sheep (1.82 kg) was heavier ( P < 0.05) than that of goats (1.46 kg). The 12-h FD group (1.74 kg) had a higher ( P < 0.05) GIT weight than the 24-h FD group (1.53 kg). Hay-fed animals had higher ( P < 0.05) rumen (7.08 vs. 6.43) and colon pH values (7.02 vs. 6.56) than those of the concentrate-fed animals. The 24-h FD group (3.39 ± 0.272 log 10CFU/g) contained more ( P < 0.05) Escherichia coli in the rumen than did the 12-h FD (2.17 ± 0.272 log 10CFU/g) group. The concentrate-fed animals (3.49 ± 0.289 log 10CFU/g) had higher ( P < 0.05) coliform counts in the rumen than the hay-fed animals (2.43 ± 0.289 log 10CFU/g). The 24-h FD group (3.42 ± 0.289 log 10CFU/g) had a higher ( P < 0.05) concentration of coliform than did the 12-h FD group (2.50 ± 0.289 log 10CFU/g). The 24-h FD group (3.31 ± 0.259 log 10CFU/g) also had higher ( P < 0.05) Enterobacteriaceae counts in the rumen than did in the 12-h FD group (2.47 ± 0.259 log 10CFU/g). Goats (5.71 ± 0.158 log 10CFU/g) had lower ( P < 0.05) total plate counts in the rumen compared to sheep (6.27 ± 0.158 log 10CFU/g). The concentrate-fed animals had higher ( P < 0.05) E. coli (6.44 vs. 4.01 ± 0.468 log 10CFU/g), total coliform (6.74 vs. 4.16 ± 0.469 log 10CFU/g), Enterobacteriaceae (6.93 vs. 3.83 ± 0.651 log 10CFU/g), and total plate counts (7.79 vs. 7.28 ± 0.170 log 10CFU/g) in the rectum than the hay-fed animals. The results indicate that microbial loads in the GIT of small ruminants may be reduced by either feeding hay for 4 d or depriving feed for 12-h prior to slaughter.