It is important to find the effective position for cough and sputum clearance in respiratory physical therapy. The purpose of this study was to compare the changes in peak expiratory flow (PEF), forced expiratory volume in 1 second ($FEV_1$), and peak cough flow (PCF) related to functional level and measurement position in patients with Duchenne muscular dystrophy. Twenty one subjects were classified into three functional levels, and measurements was undertaken in three different measurement positions (upright sitting, $45^{circ}$ reclining and supine). Vitalograph PEF/FEV DIARY was used to measure PEF and $FEV_1$, and Ferraris Pocket Peak was used to measure PCF. Mixed two-way analysis of variance and Bonferroni post-hoc test were used for statistical analysis. The results of the study were as follows: 1) Significant main effects for measurement position were found. 2) PEF was the highest in upright sitting, followed by $45^{circ}$ reclining, and supine in order. 3) $FEV_1$ in upright sitting and $45^{circ}$ reclining were significantly greater compared with that in supine. 4) PCF in upright sitting and $45^{circ}$ reclining were significantly greater compared with that in supine. 5) No significant main effects for functional level were found in PEF, $FEV_1$, and PCF. 6) No significant functional level by measurement position interactions were found in PEF, $FEV_1$, and PCF. Therefore, it is concluded that upright sitting and $45^{circ}$ degree reclining positions are recommended for effective cough and sputum clearance.