Progress has been made in understanding the malformed frog problem, yet we still cannot identify with assurance specific causes of malformations at particular locations. To address this problem we assembled a team of specialists and present here results on geographic distribution, water quality, parasite infection, and morphological patterns from Minnesota malformed frog sites and reference sites. Malformed frog hotspots (> 5% malformed animals) tend to occur in a broad line from northwest to southeast across Minnesota associated with the North Central Hardwoods and Driftless Area ecoregions, and are less associated with Lake Agassiz Plain, Northern Glaciated Plain, and Western Corn Belt Plain ecoregions. Few hotspots occur in the southwestern grassland and northeastern boreal forested portions of the state. There is a tendency for hotspots to occur at ecoregion junctions. No single water quality feature correlates with hotspots. Heavy Ribeiroia infections always indicate hotspots, but lesser Ribeiroia infections may or may not. Conversely, certain hotspots show no evidence of the presence of Ribeiroia. Among reference sites, two have no evidence of 5 Ribeiroia. The most common hindlimb malformation type was ectromelia, followed by micromelia and the presence of spongiform bone. Limb hyperextension, amelia, and polymelia were the least common malformation types. Malformed frog hotspots are typically associated with altered wetlands and any solution to the malformed frog problem must include restoring these sites.