We developed a likelihood-based method for testing for parent-of-origin effect in complex diseases. The likelihood formulations model parent-of-origin effect and allow for incorporation of ascertainment, as well as differential male and female ascertainment probabilities. The results based on simulated data indicated that the estimates of parental effect (either maternal or paternal) were biased when ascertainment was ignored or when the wrong ascertainment model was used. The exception was single ascertainment, in which we proved that ignoring ascertainment does not bias the estimation of parental effect, in a simple parent-of-origin model. These results underscore the importance of considering ascertainment models when testing for parent-of-origin effect in complex diseases.