**Exhibit 31.1**

**CERTIFICATION**

|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | I, S. Scott   Crump, certify that: |
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|           1.        I   have reviewed this annual report on Form 10-K of Stratasys, Inc. (the   “registrant”);                                                                                                                                                                                                                                                                                                                                                                               |
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|           2.        Based   on my knowledge, this report does not contain any untrue statement of a   material fact or omit to state a material fact necessary to make the   statements made, in light of the circumstances under which such statements   were made, not misleading with respect to the period covered by this report;                                                                                                                                                                 |
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|           3.        Based   on my knowledge, the financial statements, and other financial information   included in this report, fairly present in all material respects the   financial condition, results of operations and cash flows of the registrant   as of and for the periods presented in this report;                                                                                                                                                                                      |
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|           4.        The   registrant’s other certifying officer and I are responsible for establishing   and maintaining disclosure controls and procedures (as defined in Exchange   Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial   reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the   registrant and have:                                                                                                                                |
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|                      (a)       Designed   such disclosure controls and procedures, or caused such disclosure controls   and procedures to be designed under our supervision, to ensure that material   information relating to the registrant, including its consolidated   subsidiaries, is made known to us by others within those entities,   particularly during the period in which this report is being prepared;                              |
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|                      (b)       Designed   such internal control over financial reporting or caused such internal control   over financial reporting to be designed under our supervision, to provide   reasonable assurance regarding the reliability of financial reporting and the   preparation of financial statements for external purposes in accordance with   generally accepted accounting principles;                                      |
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|                      (c)       Evaluated   the effectiveness of the registrant’s disclosure controls and procedures and   presented in this report our conclusions about the effectiveness of the   disclosure controls and procedures, as of the end of the period covered by   this report based on such evaluation; and                                                                                                                      |
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|                      (d)       Disclosed   in this report any change in the registrant’s internal control over financial   reporting that occurred during the registrant’s most recent fiscal quarter   (the registrant’s fourth fiscal quarter in the case of an annual report) that   has materially affected, or is reasonably likely to materially affect, the   registrant’s internal control over financial reporting; and |
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|           5.        The   registrant’s other certifying officer and I have disclosed, based on our most   recent evaluation of internal control over financial reporting,, to the   registrant’s auditors and the audit committee of the registrant’s board of   directors (or persons performing the equivalent functions):                                                                                                                                                            |
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|                      (a)       All   significant deficiencies and material weaknesses in the design or operation   of internal control over financial reporting which are reasonably likely to   adversely affect the registrant’s ability to record, process, summarize and   report financial information; and                                                                                                                                |
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|                      (b)       Any   fraud, whether or not material, that involves management or other employees   who have a significant role in the registrant’s internal controls over   financial reporting.                                                                                                                                                                                                                                |