1. Pusat Studi Gender (PSG)
Ketua : Dr. Shinta Dewi Rismawati, S.H., M.H.
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2. Lembaga Konsultasi dan Bantuan Hukum Islam (LKBHI)
Ketua : Saif Askari, S.H., M.H
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3. Lembaga Studi Islam dan Lingkungan Hidup (LSILH)
Ketua : Maghfur Ahmad, M.Ag.
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4. Lembaga Bimbingan Konseling (LBK)
Ketua : Dr. Sopiah, M.Ag.
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5. Center for Social and Human Resources Development (CSHRD)
Ketua : Dr. Imam Kanafi, M.Ag.
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6. Lembaga Kajian dan Pengembangan Belajar Mengajar (LKPBM)
Ketua : Zaenal Mustakim, M.Ag.
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7. Lembaga Kajian dan Pengembangan Pendidikan Agama Islam (LKP2AI)
Ketua : Maskhur, M.Ag.
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8. Lembaga Riset Pendidikan (LRP)
Ketua : Drs. Slamet Untung, M.Ag.
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9. Lembaga Advokasi dan Pengembangan Ilmu Kebahasaan (LAPIK)
Ketua : Muhandis, Lc., M.A.
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10. Lembaga Survei (LS)
Ketua : H. Salafudin, M.Si.
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11. Lembaga Hisab Rukyah (LHR)
Ketua : Drs. H. Muslih Husein, M.Ag.
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12. Lembaga Dakwah Kebangsaan (LDK)
Ketua : H. Sam’ani, M.Ag.
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13. Pusat Kajian dan Pengembangan Ekonomi Syariah (PKPES)
Ketua : Ahmad Syukron, M.E.I.
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14. Lembaga Pemberdayaan Alumni Syariah (LPAS)
Ketua : Drs. Tubagus Surur, M.Ag.
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15. Lembaga Pengkajian Pengadaan Barang / Jasa Pemerintah (LP2B/JP)
Ketua : Markholis, S. Pd.I.
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