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This study aimed to evaluate the influence of maternal factors on the total plate count, Staphylococci, Lactobacilli and Bifidobacteria populations in the milk of lactating Filipino women for the first 4months of lactation period. Milk samples (n=136), 24h diet recalls and responses from a qualitative food frequency questionnaire (FFQ) were collected from 34 healthy lactating women classified according to their BMI underweight (n=7), normal weight (n=16) and overweight (n=11). The FFQ was useful in assessing prebiotic and probiotic food