The adsorption of alkaline phosphatase (AP) from buffer solutions into hydrophilic and hydrophobic methylated glass was studied qualitatively by Tapping Mode Atomic Force Microscopy (TMAFM). Three protein samples were used: soluble AP lacking GPI-anchors (AP(s)); purified AP dimer with two GPI anchors (AP(GPI)); and the same purified protein treated with acetone in order to remove all residual lipids (AP(GPI-AT)). All the preparations have a better affinity for hydrophobic surfaces and only partially maintain their enzymatic activity. The adsorption is larger for AP(GPI-AT). Adsorption and aggregation of GPI-anchored proteins on hydrophobic surfaces occurs in at least two different phases: large protein clusters adsorb rapidly on the surface (in approx. 5-10 min); and then they slowly rearrange in monolayers. The large cluster adsorption at short times suggests that the anchors favour protein aggregation in solution. AP's adsorb as individuals, which aggregate and form two-dimensional dendrites and branched structures after drying. Surfaces with GPI-anchored protein occasionally present dendrites after drying, but never surfaces iniaged in solution, It indicates that these structures are formed during drying as a result of a diffusion-limited aggregation process.