Background Most of the Leber hereditary optic neuropathy (LHON) cases are bilateral and sequential, how-ever there are rare unilateral examples, or those in which the delay of onset of vision loss between one and the other eye is longer. In the case of presumed childhood amblyopia in one eye, the vision loss in the good eye may be the only symptom of bilateral disease, that was unnoticed in previ-ously amblyopic eye, or a preexisting episode of LHON on the “amblyopic” eye. Clinical decision in such cases may be difficult and suggestive for other forms of atypical optic neuropathy until confirmed by genetic testing. Case series We present three genetically confirmed (MT-ND1:m.3700G>A, MT-ND6:m14484 T>C, and MT-ND4:m.11778G>A) patients with subacute vision loss in previously good eye with the other eye believed to be amblyopic from the childhood, and their features different of what would be expected in true amblyopia. In all, electrophysiology testing showed bilaterally reduced ampli-tude of PERG with low VEP P100 wave amplitudes and prolonged peak time in both eyes, also unusual for amblyopia. During the follow-up, pallor of the optic discs progressed in all eyes. Significant thinning of the retinal nerve fiber layer around the optic disc (pRNFL) and ganglion cell complex (GCC) in the macular region was present. All three patients had peculiar history. First patient was treated for presumed hyperopic amblyopia that did not improve since child-hood and experienced visual loss on the good eye at the age of 17 and was negative for the three typical LHON mutations. Extended testing confirmed atypical pathogenic variant MT-ND1:m.3700G>A in homoplasmy. The second patient with presumed strabismic amblyopia had unusual presentation of vision loss only at the age of 61 and after exclusion of other causes, typical MT-ND4:m.11778G>A pathogenic variant was found in homoplasmy. The third case was peculiar as he had presumed strabismic amblyopia since childhood and had some degree of disc pallor in the amblyopic eye upon presenting with loss of vision on the good eye at the age of 21 and typical pathogenic variant m14484 T>C, p.Met64Val was subsequently confirmed. However, one year after the disease onset, he started to experience significant spontaneous functional im-provement in the non-amblyopic up to 1.0 Snellen, whilst improvement in the presumed amblyop-ic eye was modest, suggesting preexisting amblyopia. This interestingly extensive improvement was carefully followed by electrophysiology as well as visual acuity and fields. Conclusion This report shows three different scenarios of presentation of LHON in patients with presumed uniocular amblyopia from childhood. In such cases, the diagnosis may be difficult and detailed structural and functional evaluation of the optic nerve head is necessary to assess whether earlier LHON episode was misdiagnosed as amblyopia or whether LHON presented bilaterally on both eyes whilst only being noticed in the previously good eye.