The overgrowth of filamentous microorganisms in wastewater treatment systems is a common adversary condition leading to foaming, poor sludge settling problems, and reduction in organic removal efficiency. Entrapped microbial cell reactors have been investigated for their uses in wastewater treatment. However, their susceptibility to filamentous growth is not known. The objective of this study is to investigate the filamentous growth and its effect on the treatment performance of an entrapped microbial cell system treating wastewater. A typical activated sludge wastewater treatment system was included for comparative purpose. Both systems were operated at the same operating conditions using synthetic wastewater. Four different hydraulic retention times (HRT) (9, 6, 3, 1.5 hours), three different dissolved oxygen (DO) concentrations (2, 4.5 and 5.7 mg/1), and three different influent chemical oxygen demand (COD) concentrations ( 120, 206 and 300 mg/I) were investigated. Results showed that DO and organic loading rate (COD/HRT) did not have any effect on the organic (soluble COD and soluble biochemical oxygen demand at 5 days) removal efficiencies at high and medium HRT (9 and 6 hours), even when there was excessive filamentous growth in the entrapped microbial cell reactor. The organic removal efficiencies of the activated sludge system dropped for some cases at high and medium HRT because of excessive filamentous overgrowth. At low HRT (3 hours), there was abundant filamentous growth and a drop in the organic removal efficiencies in the entrapped microbial cell reactor. To determine the reason (between HRT and filamentous abundance) for the decreases in organic removal efficiencies by the entrapped microbial cell system at the low HRT, a very low HRT of 1.5 hours was applied. DO and organic loading rate did not affect organic removal efficiencies of the entrapped cell reactor. Reduction of the filamentous microorganisms was attempted by chlorination using sodium hypochlorite. Three different chlorine dosages, I, 0.25 and 0.50 g NaOCl/d, were applied. The dosage of 0.25 g NaOCl/d was found to be very effective in controlling the filamentous overgrowth in the entrapped microbial cell reactor. The reduction of filamentous organisms by chlorination did not result in improved organic removal efficiencies, suggesting that the very low HRT rather than the abundance of filamentous organisms was responsible for the poorer performance of the reactor. A cell morphology and organelle analysis indicated Sphaerotilus natans as the most frequently observed filamentous microorganism in the entrapped microbial cell reactor. A thick layer of biofilm was also observed on the entrapment matrix. The biofilm did not affect the performances of the reactor. These results suggested that the entrapped microbial cell reactor is subjected to filamentous overgrowth, but it has no effect on the performances of the reactor.