Rumen ciliates still have mysterious secrets and influences in ruminants. This study investigated the effect of transfaunation of pure and mixed cultures of rumen ciliates on physical clinical examination, selected serum parameters and milk profile in defaunated lactating dairy goats. A number of 8 Baladi native breed goats were randomly classified into two groups each one containing 4 goats. Pure culture group was transfaunated with 6 ml of pure culture of Holotricha spp., while mixed culture group was transfaunated with 6 ml of mixed culture of 81.85% Holotricha and 18.15% Ophryoscolex spp. once weekly for three consecutive weeks, after defaunation of both groups using 30 ml of 8% SLS for two consecutive days. Serum and milk samples were collected weekly for three successive weeks to study effect of type of ciliate culture, duration of transfaunation and their interaction. Results revealed that transfaunation of pure and mixed cultures of rumen ciliates had no effect on physical examination with minimal non-significant improvement of calcium, inorganic phosphorous, total protein and globulin in serum of defaunated goats. Transfaunation of pure or mixed cultures of rumen ciliates within three weeks could not improve significantly decreased milk fat % of defaunated goats without any effect on other measured milk profile parameters. It is concluded that further investigations on transfaunation without prior defaunation should be performed using different pure and mixed cultures of rumen ciliates for therapeutic and productive purposes.