Evidence suggests larval yellow perch, Perca flavescens, utilize nearshore and offshore habitat during the 30–40 day period between hatch and transition from pelagic to demersal habitat. In a large, open system like Lake Michigan this represents a significant increase in available habitat and it is important to understand how this increase may impact our ability to sample larval yellow perch in an unbiased manner. We measured the vertical distribution of larval yellow perch in southern Lake Michigan as a function of size, age, and diel period. Larval yellow perch were collected from two zones (surface and epilimnion) from 1 to 32 km from shore in 2001 during the day; on four dates surface samples were also collected at night. Results indicate larval perch are more abundant at the surface at night than during the day. Larval yellow perch < 15 mm total length (TL) and younger than 18 days post hatch were found in both surface and epilimnion habitat during the day, but larvae > 15 mm TL were captured only in the epilimnion and farther than 5 km from shore, which suggests a different spatial distribution for larger, older larvae. Diel differences in larval abundance and size at the surface suggest more and larger larvae will be caught for a similar effort at night as compared to daytime sampling. Observed differences in larval distribution with size and age also suggest that sampling concentrated nearshore and/or at the surface has the potential to under-sample larger/older yellow perch larvae in Lake Michigan.