The diagnosis of first seizure or epilepsy may be challenging and misdiagnosis can occur. Studies carried out in various settings have reported misdiagnosis rates of between 4.6% and 30%. Misdiagnosis can lead to serious consequences including driving and employment restrictions and inappropriate treatments. Most studies focus on ways of reducing misdiagnosis. However, in some cases, it may be difficult to make a definite diagnosis at initial presentation. This is because of a number of reasons including overlapping clinical features with other conditions, inadequate available history and limitations of investigations. Consequently, diagnostic uncertainty is inevitable in epilepsy, although few studies acknowledge this. In this paper we review the literature on misdiagnosis rates, analyse reasons for misdiagnosis and consider limitations of available investigations. We propose that diagnostic uncertainty in epilepsy should be more widely acknowledged and addressed, and that this may reduce misdiagnosis rates.