We compared diets of juvenile lake whitefish among six sites in Lake Michigan and one in Lake Superior during 2005 and 2006 to assess spatial and temporal patterns in food habits and evaluate if ontogenetic diet shifts occur that may influence growth and survival. A total of 262 and 496 juveniles were captured in 2005 and 2006, the majority of which were captured during June and July. Sites in southern Lake Michigan tended to have larger juveniles, and the smallest juveniles were observed at Naubinway, northern Lake Michigan, and Whitefish Point, Lake Superior. The mean number of prey items per stomach differed among sampling sites and years. Copepods were the most prevalent prey item, and were present in greater than 70% of juvenile stomachs from most sites. However, the percent by number of copepods decreased during July as chironomids and other benthic macroinvertebrates increased in number. There was a significant positive relationship between percent of benthic prey items and mean length of juvenile lake whitefish. A substantial increase in the percent of benthic prey consumed after 40 mm (total length) was observed and likely resulted from juvenile lake whitefish crossing a size threshold for benthic feeding relating to morphological changes (i.e., transition of mouth opening from terminal to sub-terminal) in addition to a potential increase in the availability of emergent macroinvertebrates. Timing of the transition to benthic feeding is likely regulated by the number of prey per juvenile and the overlap with peak emergence of important benthic aquatic invertebrates such as chironomids. A better understanding of these factors will increase our understanding of juvenile lake whitefish growth and survival, which are necessary for improving year-class strength predictions.