Purpose: To investigate the association between cytokine (and related proteins) concentrations in the aqueous humor (AH) of patients with congenital cataracts and preoperative and postoperative axial length. Methods: Samples from the AH were collected from 25 eyes of 17 patients with congenital cataracts who underwent congenital cataract extraction and intraocular lens implantation. Multiplex enzyme-linked immunosorbent assays (ELI-SAs) and Luminex xMAP technology were used to assess the concentration of cytokines or chemokines, and acute phase proteins in the AH. Axial lengths were measured before surgery and at 3 months, 6 months, and 1 year after surgery. Results: The mean protein concentrations were determined in the AH of patients with congenital cataracts. The following proteins were assessed: VEGF (9.89 +/- 4.94 pg/ml), TNF-alpha (1.88 +/- 0.12 pg/ml), TGF-beta 2 (1622.88 +/- 762.53 pg/ml), IL-1RA (110.78 +/- 141.29 pg/ml), IL-1 beta (1.85 +/- 0.13 pg/ml), IL-2 (41.96 +/- 14.48 pg/ml), IL-4 (9.75 +/- 1.32 pg/ml), IL-5 (1.38 +/- 0.09 pg/ml), IL-6 (2.31 +/- 5.97 pg/ml), IL-10 (1.46 +/- 0.47 pg/ml), IL-12p70 (21.50 +/- 1.60 pg/ml), IL-15 (2.23 +/- 0.18 pg/ml), IL-17A (1.22 +/- 0.11 pg/ml), GM-CSF (2.80 +/- 0.38 pg/ml), IFN-gamma (9.20 +/- 0.42 pg/ml), CCL2/MCP-1 (131.45 +/- 90.45 pg/ml), CCL3/MIP-1 alpha (87.14 +/- 3.83 pg/ml), CCL4/MIP-1 beta (66.26 +/- 2.22 pg/ml), CXCL10/IP-10 (13.99 +/- 39.66 pg/ml), CCL11/eotaxin (27.17 +/- 2.00 pg/ml), and PDGF-BB (0.43 +/- 0.04 pg/ml). These data suggested a negative correlation between the level of VEGF in the AH and the preoperative axial length (r(2) = 0.2615, p<0.01). Similarly, the level of GM-CSF and CCL11/eotaxin in the AH decreased with an increase in axial length (r(2) = 0.2456, p = 0.01; r(2) = 0.1758, p=0.037). At 1 year post-surgery, a negative correlation was observed between the level of PDGF-BB and the change in the axial length (r(2) = 0.2133, p = 0.02). Axial elongation at 1 year post-surgery was 0.24 +/- 0.34 mm. The predicted change in axial length at 1 year post-surgery was 1.05 +/- 0.83 mm, and the actual axial elongation was statistically significantly smaller than the predicted change in healthy children (paired t test, p<0.01). Conclusions: Increased preoperative axial lengths were negatively correlated with AH levels of VEGF, GM-CSF, and CCL11/eotaxin. The level of PDGF-BB was negatively correlated with the change in axial length 1 year post-surgery. These data suggest that the concentrations of these proteins in the AH may have predictive value for changes in axial length in patients with congenital cataracts, and possibly provide a useful prognostic modality.