Introduction: Infantile nystagmus is an eye movement disorder appearing before the age of 6 months. It can be of various etiologies; however, in this age group, ophthalmic disorders predominate over neurologic ones. The major cause is albinism, followed by inherited retinal dystrophies. Nonetheless, both are umbrella terms comprising numerous diseases caused by mutations in distinct genes, of different inheritance patterns and visual outcomes, necessitating a broad genetic screening. Case report: The patient was a 4-month-old boy with infantile nystagmus and suspected of ocular albinism or early-onset retinal dystrophy. Whole-exome sequencing identified four variants in retinal dystrophy genes, two pathogenic CNGA3 mutations, corroborating the diagnosis of achromatopsia, and two concomitant ABCA4 variants, a mild and a frequent hypomorphic allele. Based on the existing genotype-phenotype correlations and considering the visual limitations associated with a primary diagnosis, the detected ABCA4 variants were assumed unlikely to be significant for the patient’s visual functioning. Conclusions: The present case highlights the need for judicious evaluation of multiple variants detected via high-throughput genetic testing methods and cautions against hasty diagnoses. The mere identification of a biallelic mutation in a recessive disease-associated gene is not always sufficient to make a diagnosis, as in this instance, a diagnosis of Stargardt disease was not justified, given the mild character of the variants. Moreover, even a postulated association with age-related macular degeneration or late-onset macular dystrophic changes, considering the achromatopsia phenotype, appears to be of limited relevance for the patient, thereby underscoring the necessity of an individualized approach to each case.