The survival rates of Lactobacilus acidophilus Ki, Lactobacillus paracasei L26 and Bifidobacterium animalis BB-12 were studied after whey protein microencapsulation via spray-drying, with or without l-cysteine-HCl, and storage up to 6 months at 5 °C and 22 °C, with variation in relative air humidity and oxygen levels. Lb. paracasei L26 was the least susceptible to storage conditions: above 106 cfu g-1 were recorded by 180 d at 22 °C, irrespective of relative humidity, and the presence/absence of oxygen and l-cysteine. Higher relative humidity, higher temperature and longer storage periods were deleterious to survival of both B. animalis BB-12 and Lb. acidophilus Ki; the effect of l-cysteine-HCl was dependent on the probiotic strain. The effect of overhead oxygen was not significant upon any probiotic strain studied. Whey protein microcapsules containing l-cysteine-HCl protected probiotic cultures from simulated gastrointestinal conditions.