The aim of this study was to assess the prevalence of coexistent ocular pathology and identify / describe the factors that contribute to undiagnosed alternate diagnosis and / or co-existent pathology at initial presentation in patients referred as potentially amblyopic. This was a retrospective study with children grouped to A: primary diagnosis of amblyopia, and B: final diagnosis of coexistent alternative pathology. Of 482 children with an initial diagnosis of amblyopia, and with sufficient follow-up and ophthalmic examinations, 466 had a final diagnosis of amblyopia alone and 26 had persistent reduced best corrected visual acuity. Of 26 children, six had a re-diagnosis of alternative condition - two keratoconus and four cases of subclinical optic neuropathy. The remaining 20 children had alternative aetiology for their reduced visual acuity including eight cases of ametropic amblyopia - the most frequent alternative diagnosis - seven with anisometropic amblyopia, three stimulus deprivation and three strabismic amblyopia. Median time to establishing the alternative diagnosis was 18.5 months (range 3-34). Final alternative diagnosis / co-existent pathology included occult macular dystrophy (n=10), subclinical optic neuropathy (n=13), keratoconus (n=2) and juvenile retinoschisis (n=1). The most common clue to alternative diagnosis was lack of visual acuity improvement despite good compliance (n=21). Median best corrected visual acuity was 0.45logMAR after six months follow-up. Median time of amblyopia treatment was 9.5 months. Other clues included subtle optic disc pallor (n=11), reduced colour vision (n=7), history of parental consanguinity (n=7) and preceding febrile illness (n=1). For those diagnosed with optic neuropathy, they showed reduced colour vision (n=7), disc pallor (n=10), visual field reduction (n=13) and visual evoked potentials (VEP) abnormalities (n=9). For cases of occult macular dystrophy, all had reduced central responses on mfERG. Overall, a final alternative diagnosis was made for 5.1% of children. The authors highlight the importance of careful ophthalmic examination where improvement of visual acuity with amblyopia therapy is not as expected, despite good compliance.