This chapter explores the use of one-way between-groups multivariate analysis of variance (MANOVA) to investigate the effects of gender on perceived English language ability challenges in an English Medium Instruction (EMI) university in Hong Kong. Contrasting with ANOVA which evaluates mean differences on one dependent variable, MANOVA evaluates if there are mean differences on two or more dependent variables. The two dependent variables used were perceived writing challenges and perceived speaking challenges. The independent variable was gender. We checked for univariate and multivariate outliers, homogeneity of variance-covariance matrices and normality and found no deviation from the standard parameters. The results show a significant difference between males and females in terms of the combined dependent variables, F (2, 75) = 3.444, p = 0.037, Wilks’ Lambda = 0.913 and partial eta squared = 0.087. When the dependent variable is analysed separately with reference to the Bonferroni adjusted alpha level of 0.025, a significant difference is only found between males and females in terms of the perceived speaking challenges, F (1, 75) = 6.658, p = 0.012, partial eta squared = 0.084. A closer examination of the mean score shows that females (M = 3.042, SD = 0.34) perceived speaking English to be more of a challenge than males did (M = 2.71, SD = 0.55). The findings are discussed in relation to teaching and learning in an EMI university.