Diagnosis of a disease is one of the most important processes in the field of medicine. Thus, computer-aided detection systems are becoming increasingly important to assist physicians. The iron deficiency anemia (IDA) is a serious health problem that requires careful diagnosis. Diagnosis of IDA is a classification problem, and there are various studies conducted. Researchers also use feature selection approaches to detect significant variables. Studies so far investigate different classification problems such as outliers, class imbalance, presence of noise, and multicollinearity. However, datasets are usually affected by more than one of these problems. In this study, we aimed to create multiple systems that can separate diseased and healthy individuals and detect the variables that have a significant effect on these diseases considering influential classification problems. For this, we prepared different datasets based on the original dataset whose outliers were removed using different outlier detection methods. Then, a multistep classification algorithm was proposed for each dataset to see the results under irregular and regulated conditions. In each step, a different classification problem is handled. The results showed that it is important to consider each question together as it can and should change the outcome. Dataset and R codes used in the study are available as supplementary files online.