Many systems are available for the isolation of anaerobic bacteria from clinical specimens. The jar system is the oldest and more adapted while the pouches are not popular with many investigators. The anaerobic chambers are expensive to maintain and technically inflexible. This study evaluated the efficacy of the Oxoid anaerobic jar and the GENbag pouches as anaerobic incubation systems. Anaerobic cultures were set up for 145 middle ear exudates and incubation was in the anaerobic jar, GENbag or a combination of both. The effect of specimen transport system and time lapse before culturing on the performance of the anaerobic systems were evaluated Ten genera of anaerobic bacteria were isolated with both systems (P &gt; 0.05). <em>Peptostreptococcus</em> and <em>Prevotella</em> were isolated more frequently in Oxoid jar than in GENbag (P &lt; 0.05) but both systems were not discriminatory for <em>Clostridium</em>, <em>Propionibacterium</em> and <em>Veillonella</em>. The use of GENbag as a backup to Oxoid jar increased isolation rate from 56.6% to 90.3% (P &gt; 0.05). Type of transport media or vehicle did not affect the recovery of anaerobes adversely as did delay in processing of specimen. A careful application of a number of variables may improve isolation of anaerobes from clinical specimens