The start-up of an Anammox process was studied in a membrane sequencing batch reactor (MSBR) in which a submerged hollow fibre membrane module was used to retain the biomass. The reactor was seed with Anammox biomass and fed using the Van de Graaf medium. During a first operating stage, salt precipitation was observed and interfered with microbial activity and caused a decrease of the nitrogen removal rate of the reactor from 100 to only 10 mgl(-1) per day. Salt precipitation was avoided by diminishing adequately the Ca and P concentrations of the Van de Graaf medium during the last operating stage. This action increased quickly the activity of the system, and nitrogen removal rate reached up to 710 mgl(-1) per day with almost full nitrite removal. Sporadic flotation of the sludge was observed in the MSBR. The use of the membrane avoided biomass wash-out from the system. Moreover, a surprising fact was that Anammox biomass did not grow in flocs in the MSBR, but in granules. This fact showed that this kind of microorganisms have a trend to grow in aggregates. Results indicated that the use of the MSBR could be a suitable system for nitrogen removal by using the Anammox reaction.