Objective: The objective of this study is to evaluate the wall adaptation and apical microleakage values following the application of various irrigation protocols in primary teeth. Material and methods: For the two parts of the study, extracted upper incisor primary teeth were randomly included to the 1% sodium hypochlorite (NaOCl), 10% ethylenediaminetetraacetic acid (EDTA)+1% NaOCl, 6% citric acid (CA)+1% NaOCl and 0.9% physiological saline (PS) groups. Canal wall adaptation and apical microleakage were assessed by scanning electron microscopy (SEM) and stereomicroscope, respectively. Results: 6% CA + 1% NaOCl group was found to be the most successful irrigation protocol in providing strong canal wall adaptation and less apical microleakage, followed by 10% EDTA +1% NaOCl. 6% CA +1% NaOCl was significantly superior regarding apical microleakage (p < .05). Conclusions: Due to the ability to provide appropriate changes in the root canal walls to make a well-adapted and leak-proof canal filling, 6% CA + 1% NaOCl can be recommended as an irrigation protocol in primary teeth.