Background: The pollen of Parietaria spp., a weed of the Urticaceae family, is a major cause of respiratory allergy in the Mediterranean area, where the most common species are Parietaria judaica and Parietaria officinalis. In this study, we evaluated the specific serum IgE-binding profiles to individual P. judaica pollen recombinant major allergen, and Phleum pratense cytoskeletal profilin and a 2-EF-hand calcium-binding allergen homologous to cross-reactive Parietaria pollen allergens, in patients allergic to pollen with positive skin test towards Parietaria spp. extract. Methods: The present observation included 220 patients from the province of Cuneo, north-west Italy, all suffering from rhino-conjunctivitis and/or asthma selected on the basis of skin test positive to P. judaica extract. The sera were evaluated for specific IgE reactivity to P. judaica pollen major recombinant(r) allergen Par j 2, Phleum pratense pollen allergens rPhl p 7 (2-EF-hand calcium binding protein) and rPhl p 12 (profilin), both identified as cross-reactive Parietaria spp. allergens, using Pharmacia CAP System. Out of 220 patients, 37 patients with IgE reactivity to rPar j 2 and 105 patients sensitized to at least one timothy pollen major allergen (i. e. rPhl p 1, rPhl p 2, natural Phl p 4 and rPhl p 6) were submitted to an ultra-rush protocol of sublingual immunotherapy (SLIT). The occurrence of adverse reactions were evaluated in both groups. Results: All 220 patients with pollinosis and positive in vivo skin prick tests had in vitro positive CAP results to P. judaica natural extract. On the contrary, in these patients the prevalence of Par j 2-specific IgE was only 33.2% (73/220). In fact, 116/220 (52.7%) patients with serum specific IgE to crude Parietaria pollen extract had specific IgE to Phl p 12, 18/220 (8.1%) subjects with specific IgE to rPhl p 12 also exhibited specific IgE to Phl p 7 and 26/220 (11.8%) subjects had specific IgE against rPhl p 7. Particularly, geometric mean (25th–75th percentile) of specific IgE to rPar j 2 were as follows: 2.87 kUA/l (1.005–7.465). Out of 73 patients with specific IgE to rPar j 2, 7 subjects (9.6%) had also specific IgE to rPhl p 7, 12 (16.4%) had specific IgE to rPhl p 12 and 4 (4.1%) patients had specific IgE to both recombinant allergens. Of 37 patients under an ultra-rush protocol of SLIT, 3 subjects (8.1%) experienced generalized urticaria, and 1 of them also had diarrhea 3 h after the last dose of Parietaria judaica extract oral-vaccine administration. On the contrary, no systemic reactions were observed in 105 patients after Phleum pratense extract oral intake after a similar ultra-rush SLIT protocol (p = 0.0046). Conclusions: In the light of present findings, allergen extract-based diagnosis, in vivo and in vitro, cannot discriminate allergic patients that are genuinely sensitized to Parietaria spp. major allergens or to other major allergens to which current immunotherapeutic allergy extracts are standardized. Therefore, in vitro component resolved diagnosis is the unique tool to define the disease eliciting molecule(s). Finally, during sublingual immunotherapy, not only the dose of allergen, but also the biochemical characteristic of the major allergen administered may be an important factor in determining possible systemic reactions.