I am comparing two groups on three levels and felt a MANOVA analysis would effectively analyze the data. One group has 40 participants and the other 180 participants due to the nature of the groups. This is unavoidable. Will the in-equivalent groups jeopardize the integrity of the study, or is there another test that would be better to evaluate the data?

Hello

Mixed effects models (otherwise known as multilevel models) or just simple regression would better analyze the data, as it can deal with unequal groups. You would treat group as a predictor with two levels (i.e., group 1, group 2).

But what do you mean by "on three levels"? Three dependent variables/outcomes (e.g., score 1, score 2, score 3), or one dependent variable/outcome with three levels (e.g., ill, healthy, deceased)? This will affect your choice of analysis.

Tudor