Mannose-binding protein (MBL) is a critical component of innate immunity and provides first-line protection against pathogens by binding to N-acetyl-glucosamine and mannose residues on the surface of microorganisms (bacteria, fungi and parasites). MBL can activate complement by the lectin pathway. Both circulating MBL serum levels and functional activity have been correlated with common genetic variants in the MBL2 gene; decreased levels and activity correlate with 3 nonsynonymous single nucleotide polymorphisms, SNPs, (known as B, C and D) in exon 1 and two linked promoter SNPs (−550 H/L and −221 Y/X) as well as a 5′UTR SNP (+4 P/Q) influence circulating levels. These components form the “secretor haplotypes”, which correlate with circulating levels. A number of studies have reported associations between MBL deficiency and recurrent or severe infections, especially in immuno-incompetent patients (i.e., BMT recipients, cancer patients, and infants) or in auto-immune disorders; however, measured MBL serum levels do not fully correlate with the “secretor haplotypes”. Based on data from a re-sequence analysis across the entire MBL2 locus, in which we revealed a probable recombination hotspot in the 3′ end of the gene dividing MBL2 into two haplotype blocks, we investigated whether the extended block structure might identify additional SNPs that contribute to MBL serum levels and activity. We analysed more than 20 common SNPs across the locus, including haplotype-tagging SNPs (htSNPs) with Taqman assays validated on the SNP500 website (http://snp500cancer.nci.nih.gov); we captured more than 95% of common haplotypes in both the 5′ and 3′ haplotype blocks. Our pilot analysis was performed in 235 DNA samples of healthy Dutch Caucasian blood donors with known MBL serum concentrations measured by ELISA. Haplotypes were deduced by maximization-estimation analysis of unphased genotypes; PHASE 2.0 (http://www.stat.washington.edu/stephens/software.html). The haplotype analysis of the results confirmed the haplotype block structure of MBL2 in the Dutch population. The additional 5′ variants tested in this study were in strong linkage to the elements of the “secretor haplotypes”; functional alleles B, C and D also lie on restricted haplotypes. As reported by others, in our study, the secretor haplotypes predicted levels in roughly 85%. Four variants in the 3′ block (Ex4–1483T>C, Ex4–1067G>A, Ex4–901G>A and Ex4–710G>A) lie in 3 common haplotypes (TAAA, CGGG and TGAA) that strongly correlate with MBL serum concentration (Kruskal-Wallis p < 0.0001); individuals with at least one TAAA allele have a higher serum concentration. Thus, it is also possible that both 5′ and the 3′ haplotypes could contribute to serum levels. This suggests that there could be a selective advantage for diversification of the 3′ region of the gene, perhaps altering expression or stability (to be analyzed in follow-up studies). Our data provide evidence that there are additional SNPs in regulatory elements of MBL2, which could influence circulating levels. These observations could improve the predictive value of locus-wide analysis of MBL2 in genetic association studies.