<PAGE>
 
                                  EXHIBIT 11.1

                    INTERCELL CORPORATION AND SUBSIDIARIES
                       COMPUTATION OF NET LOSS PER SHARE
<TABLE> 
<CAPTION> 
 
                                                                Three months ended March 31      Six months ended March 31
                                                                    1998            1997            1998            1997
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<S>                                                           <C>               <C>            <C>              <C>
Loss from continuing operations                                   ($2,022,000)   ($1,718,000)     ($5,267,000)   ($3,851,000)
Deemed preferred stock dividend relating to
   in-the-money conversion terms                                      (15,000)      (496,000)         (30,000)      (717,000)
Accrual dividends preferred stock                                     (37,000)                        (37,000)
Accretion on preferred stock                                          (29,000)      (155,000)         (64,000)      (295,000)
                                                            ----------------------------------------------------------------
Loss from continuing operations applicable to common               (2,103,000)    (2,369,000)      (5,398,000)    (4,863,000)
 shareholders
 
Discontinued operations
  Gain/(loss) from discontinued operations                           (461,000)       259,000         (215,000)       470,000
  Loss on sale of subsidiary                                         (350,000)                       (350,000)
                                                            ----------------------------------------------------------------
Loss from discontinued operations                                    (811,000)       259,000         (565,000)       470,000
 
Net loss applicable to common stockholders                        ($2,914,000)   ($2,110,000)     ($5,963,000)   ($4,393,000)
                                                            ================================================================
 
Weighted average number
of common shares outstanding                                       32,061,656     17,789,405       30,222,670     16,996,221
 
Net loss per common share:
   Loss from continuing operations                                     ($0.07)        ($0.13)          ($0.18)        ($0.29)
   Loss from discontinued operations                                   ($0.02)    $     0.01           ($0.02)    $     0.03
                                                            ----------------------------------------------------------------
Net loss per applicable to common stockholders                         ($0.09)        ($0.12)          ($0.20)        ($0.26)
                                                            ================================================================
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Diluted loss per share is not presented as the effect of the potential
conversion of preferred stock to common stock and the exercise of outstanding
warrants and options would decrease loss per share.


              SEE NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS.