Accuracy of malaria diagnosis by microscopy has been a challenge in Nigeria due to poor competence of microscopists and inability to report on malaria species other than Plasmodium falciparum. Short courses were conducted to improve the skills of laboratory personnel to perform malaria microscopy in public health facilities. Seven-day malaria microscopy courses were conducted annually between 2011 and 2013.The training courses contained theoretical and practical sessions. Impact of the training was evaluated by practical and theoretical pre- and post-training assessments on malaria slide reading, parasite enumeration and basic malariology. The 102 participants who completed the training consisted of medical laboratory scientists (62; 60.8%), medical laboratory technicians (24; 23.5%) and other healthcare workers (16; 15.7%). The knowledge of basic malariology (theory) at pre- and post-tests were 34% (95% CI 31.7-36.3%) and 74.9% (95% CI 71.8-78.0%), respectively (P<0.001). The mean slide reading detection, species and counting agreements in pre-training assessment were 48.9%, 27.9% and 0%, respectively, and in post-training 56.8%, 39.2% and 25%, respectively. The mean species agreements in picture test pre- and post-training were 21.9% and 55.1%, respectively. There were significant differences (P<0.05) in the median pre-test scores in picture tests and basic malariology of the three categories of participants but not in malaria slide reading and parasite counting tests. However, post-training, a significant difference in test scores of the three categories of participants was recorded only for basic malariology (P=0.0003). The 7-day malaria microscopy courses significantly increased the knowledge and microscopy skills of the trainees and were sufficient to bridge the significant difference in baseline microscopy skills of the different categories of trainees that participated in the training courses.