BACKGROUND Milk is a common infant food in peri-urban Kenya that can transmit diarrhea-causing enteric pathogens. Little is known about how contamination of milk at point of purchase and household handling of milk-based infant foods contribute to infant exposure to enteric pathogens. OBJECTIVE To compare the prevalence and concentrations of bacterial indicator organisms and enteric pathogens in unpackaged, fresh pasteurized, and ultra-high temperature (UHT) treated milk at purchase and assess the influence of the type of milk used to prepare infant food on contamination of this food. METHODS Paired samples of purchased milk and infant food prepared with this milk were obtained from 188 households in low-income neighborhoods in Kisumu, Kenya. Samples were cultured on selective media to isolate Salmonella enterica, Shigella spp., Klebsiella aerogenes, Proteus spp., and Escherichia coli, with pathogens validated by PCR. Probability of detection of these bacteria was compared by milk product treatment and packaging method, and between milk at point of purchase vs. food at point of infant consumption. RESULTS Unpackaged milk was most contaminated at point of purchase, but bacterial contamination was also present in pasteurized and UHT milk at purchase. Presence of bacteria in UHT and fresh pasteurized milk at purchase predicted presence of the same bacteria type in infant food. Prevalence of bacterial contamination and concentration level for bacterial indicators generally increased between point of purchase and consumption in UHT and fresh pasteurized milk-based food but decreased in unpackaged milk-based food. Prevalence of the four fecal bacteria were similar in infant foods prepared with each type of milk. CONCLUSIONS Both pre-market contamination and post-purchase handling influence the likelihood of infants ingesting foods contaminated by diarrheal pathogens.