Autoimmune Lymphoproliferative Syndrome Database (ALPSbase): Database of mutations causing human ALPS
http://research.nhgri.nih.gov/alps/

AntiJen is a database system focused on the integration of kinetic, thermodynamic, functional, and cellular data within the context of immunology and vaccinology.
http://www.ddg-pharmfac.net/antijen/AntiJen/antijenhomepage.htm

Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases.
http://www.iedb.org/

Mutation registry for X-linked agammaglobulinemia.
http://bioinf.uta.fi/BTKbase/

Database about the human immune response to cancer.
http://www2.licr.org/CancerImmunomeDB/

The dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC).
http://www.ncbi.nlm.nih.gov/mhc/MHC.cgi?cmd=init

EPIMHC is a relational database of MHC-binding peptides and T cell epitopes that are observed in real proteins. Currently, the database contains 4867 distinct peptide sequences from various sources, including 84 tumor-associated antigens.
http://bio.dfci.harvard.edu/epimhc/

Epitome is a database of all known antigenic residues and the antibodies that interact with them, including a detailed description of residues involved in the interaction and their sequence / structure environments. Additionally, Interactions can be visualized using an interface into Jmol.
http://www.rostlab.org/services/epitome/

The HIV Molecular Immunology Database is an annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites. These data are also printed in the HIV Molecular Immunology compendium which is updated yearly and provided free of charge to scientific researchers. The goal of this database is to provide a comprehensive listing of defined HIV epitopes.
The database is operated by the University of California for the US Department of Energy.
http://www.hiv.lanl.gov/content/immunology/index.html

Database about the HLA-system.
http://bio.dfci.harvard.edu/Database/db_show_hla.html

X-linked severe combined immunodeficiency (XSCID or X-SCID) is an immune disorder caused by mutations in the X-linked gene IL2RG, which encodes the common gamma chain (c) of the lymphocyte receptors for interleukin-2 (IL-2) and many other cytokines. A database of human XSCID mutations (IL2RGbase) has been assembled. Information on new mutations may be submitted online.
http://research.nhgri.nih.gov/scid/

The international ImMunoGeneTics information system (IMGT; http://imgt.cines.fr), is a high quality integrated information system specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGenetique Moleculaire (LIGM; Universite Montpellier II and CNRS) at Montpellier, France
http://www.ebi.ac.uk/imgt/

IMGT/3Dstructure-DB and IMGT/Structural-Query are a 3D structure database and a tool for immunological proteins. They are part of IMGT, the international ImMunoGenetics information system, a high-quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species, which consists of databases, Web resources and interactive on-line tools.
http://imgt3d.igh.cnrs.fr

Informations about vertebrate immunoglobulin and T cell receptor genes.
http://www.imgt.org/genedb/

The IMGT/HLA Sequence Database is a database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO HLA Nomenclature Committee for factors of the HLA System. The IMGT/HLA Sequence Database is part of the international ImMunoGeneTics project (IMGT).
http://www.ebi.ac.uk/imgt/hla/

Informations about the Familial Mediterranean Fever and hereditary autoinflammatory diseases.
http://fmf.igh.cnrs.fr/infevers/

The MHC Haplotype Project is a framework and resource for association studies of all MHC-linked diseases. It will provide the complete genomic sequences of at least 8 different HLA-homozygous typing haplotypes, their resulting variations (SNPs and indels) and ancestral relationships.
http://www.sanger.ac.uk/HGP/Chr6/MHC/

MHC-Peptide Interaction Database (MPID) provides structural information and characterization of MHC peptide interaction on major histocompatibility complex of both class I and class II.
http://surya.bic.nus.edu.sg/mpidt/

This Database contains information on:

VBASE2 is a database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences.
http://www.vbase2.org/