The Gram-negative bacterium Stenotrophomonas maltophilia is frequently isolates from pharmaceutical facilities, especially in water systems. The biofilms formed by these microorganisms help them to acquire greater resistance to the action of physical and chemical agents, which may contribute to the prevalence of these pathogens in some environments. After biofilm formation, additional microorganisms can proliferate by aggregation and detach from the surface in different stages of the production chain. This event can limit the efficiency of random sampling in quality control and affect the release of a batch. This study aimed to evaluate the aggregative capacity and the structure of the biofilm by Scanning Electron Microscopy (SEM). The evaluation of aggregative capacity was performed using brain-heart infusion broth incubated at 37ºCunder static and agitation conditions. Biofilm formation assay was performed on 2.0 cm diameter stainless-steel discs. After biofilm formation and treatment, samples were washed and fixed. Then, samples were dehydrated in crescent series of acetone. Ultrathin sections were stained and observed using an electron microscopy. All strains presented sediment < 0.1 mL in both incubation conditions and were classified as non-aggregative. SEM revealed that S. maltophilia formed biofilms characterized by homogeneous distribution of bacteria’s on the surface with the formation of few aggregates for all strains analyzed, except one. The analysis by SEM showed small aggregates, although the strains were classified in this study as non-aggregative. This information may be of great use for the pharmaceutical facility, since the formation of these small aggregates can impact on intermittent contamination at different steps of the production chain, due to their detachment from the surface. The SEM seems to be an efficient technique that can be applied for biofilm understanding and can be used as part of the contamination control strategy of the pharmaceutical facility to developing of preventive and corrective measures to eliminate microbial biofilms on stainless-steel surfaces.