Micro-encapsulation is a method of providing probiotic living cells with a physical barrier against adverse environmental conditions. Lactobacillus acidophilus is one of the most effective forms of probiotic bacteria and is commercially available as pure culture and encapsulated form. It is not clear whether the use of micro-encapsulated L. acidophilus will result in yogurt of a better quality compared to non micro-encapsulated L. acidophilus. The objective was to determine the influence of micro-encapsulated L. acidophilus on the characteristics of fat free plain yogurt. Yogurt mixes were pasteurized and at 37˚C were inoculated with Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus and micro-encapsulated L. acidophilus R0052 or non micro-encapsulated L. acidophilus R0052. Yogurt manufacture was replicated three times. Yogurts with micro-encapsulated L. acidophilus R0052 had significantly (P < 0.05) higher flavor scores, compared to yogurts with non micro-encapsulated L. acidophilus R0052. The L. acidophilus counts, apparent viscosity, pH and syneresis, of the yogurts with micro-encapsulated L. acidophilus R0052 were not significantly (P < 0.05) different from those of the yogurts with non micro-encapsulated L. acidophilus R0052. Use of micro-encapsulated L. acidophilus R0052 resulted in better tasting yogurts probably because of the taste imparted by the trace amounts of the micro-encapsulating material.