A mixed effects model, enhanced by a Kronecker product structure for the residual variance-covariance matrix, is used in conjunction with a discriminant analysis technique, to devise a new statistical classification method on incomplete doubly multivariate data. The proposed method is efficient in small scale clinical trials that use relatively few patients. The new classification method is also applied to multiply imputed data sets. The misclassification error rates (MERs) are compared in order to investigate the effectiveness of the new classification rule on an incomplete data set. The classification method is applied to a real data set. The error rates on the incomplete data set are found to be much less than the median error rate on the multiply imputed data sets. Non-parametric methods, such as kernel method and k-nearest neighbourhood method, are also applied to multiply imputed data sets. Results illustrating the advantages of the new classification method over classic non-parametric classification methods are presented.