We report on a 3-year-old boy who has congenital adrenal hyperplasia and a suspected Van Maldergem syndrome, another genetic condition, with the classic phenotype seen in our patient. The latter diagnosis was supported by a genetic test that showed a novel and likely pathogenic variant in a previously described gene of the syndrome. Paediatricians do encounter such a challenge of coexisting genetic conditions albeit infrequently, and advanced genetic analysis, example whole exome sequencing, increasingly report variants of unknown significance with a variable degree of potential pathogenicity. The treating physician needs to follow a systematic approach and entertain thorough literature search and brainstorming in order to prove or disprove any possible relationship between coexisting genetic conditions. The first step should be confirming the existence of the two conditions in the first place. In addition, when family segregation is unable to confidently make a sensible conclusion in such cases, a clinician should proceed to advanced functional studies to confirm pathogenicity. Then, one can explore further any hidden relationship between coexisting and possibly clinically-related genetic conditions.