Abstract Minimum variance analysis of the magnetic field (MVAB), among various techniques of planar structure analysis, is most widely used for its numerical simplicity and loose requirements for data. Through a large number of studies based on MVAB, a global picture of the solar wind intermittency has been established. However, the huge discrepancy between the results from MVAB and other techniques like timing/triangulation implies that the uncertainty of MVAB is a crucial issue that is not fully understood. Utilizing Cluster data, we establish a data set comprised of 6752 discontinuities, whose orientations are precisely determined by timing, as a benchmark for testing MVAB. We find that the scatter of the MVAB normals around the timing normal can be reduced by elevating the threshold for the eigenvalue ratio λ 2 / λ 3 and narrowing the data window to which MVAB is applied. The misidentification of discontinuities with B N / ∣ B ∣ < 0.4, Δ∣ B ∣/∣ B ∣ < 0.2 as rotational discontinuities (RDs, identified by B N / ∣ B ∣ > 0.4, Δ∣ B ∣/∣ B ∣ < 0.2) is proved to be a major and inherent defect of MVAB, which can occur even when λ 2 / λ 3 is large. Such a misidentification process is revealed to be related to a special discontinuity geometry. It also explains the false RD predominance reported by previous studies based on MVAB. Finally, we provide advice for the application of MVAB and discuss the possibility of obtaining the real statistical properties of interplanetary discontinuities by using MVAB.