The UNICEF conceptual framework for child undernutrition indicates that malnutrition occurs as a result of inadequate dietary intake and disease. Exclusive breastfeeding for six months is the "gold standard" in infant feeding, yet the majority of women in sub-Saharan Africa do not practice EBF for the recommended duration. Additionally, diarrhea remains one of the leading causes of child death in developing countries, with Cryptosporidium as one of the most common diarrhea-causing parasites. Despite the health consequences of Cryptosporidium infection in childhood, little is known about the natural history of and risk factors associated with infection. The aim of this study was to determine the prevalence of Cryptosporidium in mothers and infants up to six months post-partum and the factors associated with infection, namely duration of exclusive breastfeeding and immune composition of breast milk. In a prospective cohort of 125 mothers and infants we found that maternal post-partum prevalence of Cryptosporidium was high, yet prevalence of infant infection remained low until six months of age. Factors associated with an increased risk of infant Cryptosporidium infection included maternal Cryptosporidium infection and maternal hand washing prior to infant feeding. We also saw increases in infant Cryptosporidium infection that corresponded to changes in infant feeding patterns. Using the same cohort of mothers, we collected breast milk and blood samples to determine how concentrations of immunoglobulins and cytokines evolved over the six months post-partum period. We found that there were no differences in breast milk immune composition based on maternal HIV-status or maternal nutritional status. However, we did find that concentrations of breast milk immunoglobulins increased as the duration of exclusive breastfeeding increased and with increased breastfeeding frequency. Breast milk cytokine concentrations were associated with indicators of maternal illness, such as mastitis and fever. Finally, we explored the relationship between infant feeding patterns and breast milk immune concentrations to determine if they were associated with infant Cryptosporidium infection. We found that an increased duration of exclusive breastfeeding and higher doses of breast milk immunoglobulins and cytokines were associated with a decreased risk of infant Cryptosporidium infection, while the feeding of certain complementary foods was associated with an increased risk of infection. We conclude that Cryptosporidium is an important gastrointestinal parasite in this region of Tanzania. The research underscored the importance of appropriate infant feeding in the first six months as optimal infant feeding behaviors were associated with both an increase in breast milk immune molecules as well as a decreased risk of infant Cryptosporidium infection.