The phosphatidylinositol-3-kinase/AKT (PI3K/AKT) pathway is commonly deregulated in breast cancer through several mechanisms, including PI3K catalytic subunit alpha (PIK3CA) mutations and loss of phosphatase and tensin homolog (PTEN). The hiperactivated PI3K/AKT signaling can be associated with endocrine or trastuzumab therapy resistance and underscore the impact of targeting the pathway. Our aim was to identify PIK3CA mutations and the mechanisms of PTEN loss and assess their therapeutic consequences in breast cancer patients. In addition, we aimed to identify further possible therapeutic targets associated with PTEN loss. Sixty-nine primary breast cancer samples (24 ER+/PR+/HER2-, 20 HER2+ (ER-/PR-/HER2+) and 25 triple-negative (TN) samples) were studied. We determined the PTEN mRNA levels, PTEN and PIK3CA mutations, PTEN allelic loss and promoter hypermethylation. mRNA expression patterns of PTEN knocked out and wild type MCF10A cell lines were compared using oligonucleotide microarray and their sensitivity to FGFR1 inhibitor PD166866 was tested. Elevated PI3K/AKT pathway activity was found in 68% of TN and about 45% of ER+/PR+ and HER2+ tumors. PTEN loss was dominant in TN and HER2+ tumors, while PTEN loss and PI3K activation were equally represented in ER+/PR+ cancers. The coexistence of PTEN loss and PI3K activation was typical of a portion of HER2+ tumors. The PTEN-deficient MCF10A cell line showed increased expression of certain members of the fibroblast growth factor 2 (FGF2)/FGFR1 pathway. We suppose that loss of PTEN enhances the autocrine FGF signaling promoting cell proliferation. FGF-2 and FGFR1 can be potential targets in PTEN deficient breast cancers.